A GenomeSpace orientation webinar will be held October 24, 2016, from 2:00-3:00PM EDT (18:00-19:00 UTC/GMT).

In this webinar, we will walk users through the GenomeSpace User Interface (GSUI) and introduce users to the GenomeSpace Recipe Resource. We will cover what a recipe is, how to search for recipes of interest, how to use a recipe, and how to create your own recipes. As a part of this, we will be doing a live demonstration of running a recipe in GenomeSpace.

Space for the GenomeSpace Orientation Webinar is now filled. The webinar will be recorded and the link will be posted, for those that are unable to attend the live session. We will be hosting more orientation webinars soon, so if you missed this round, there will be another chance! Check out the GenomeSpace Calendar of Events for upcoming webinar, office hours, and other outreach events.

Thank you to those of you who joined us for our GenomeSpace recipe webinar on June 27, 2016. If you missed the webinar, don't worry! A recording of the webinar is available on our YouTube channel. While you're there, check out our recipe videos and other helpful guides.

For future reference, links to webinar recordings will be made available in the webinar event descriptions on the GenomeSpace calendar.

GenomeSpace is proud to announce the addition of a new data resource to the GenomeSpace tool catalog: FireBrowse.

FireBrowse is a companion portal to the Broad Institute GDAC Firehose analysis pipeline. Developed for The Cancer Genome Atlas (TCGA), and backed by a powerful compute infrastructure, programming interface, online reports and modern graphical tools, FireBrowse provides a simple yet capable means of visually and programmatically exploring one of the most comprehensive and deeply-characterized open cancer datasets in the world. FireBrowse is developed at The Broad Institute of MIT and Harvard.

Thank you to those of you who joined us for our GenomeSpace webinar last week (Feb 29, 2016). If you missed the webinar, don't worry! A recording of the webinar is available on our YouTube channel. While you're there, check out our recipe videos and other helpful guides.

For future reference, links to webinar recordings will be made available in the webinar event descriptions on the GenomeSpace calendar.

The first GenomeSpace orientation webinar will be held February 29, 2016, from 2:00-3:00PM EST (19:00-20:00 UTC/GMT).

In this webinar, we will walk users through the GenomeSpace User Interface (GSUI) and introduce users to the GenomeSpace Recipe Resource. We will cover what a recipe is, how to search for recipes of interest, how to use a recipe, and how to create your own recipes. As a part of this, we will be doing a live demonstration of running a recipe in GenomeSpace.

Space for the GenomeSpace Orientation Webinar is now filled. The webinar will be recorded and the link will be posted, for those that are unable to attend the live session. We will be hosting more orientation webinars soon, so if you missed this round, there will be another chance! Check out the GenomeSpace Calendar of Events for upcoming webinar, office hours, and other outreach events.

All members of the GenomeSpace community can now author and share recipes with each other. We invite you to contribute your own analysis recipes and add your comments and votes to other recipes. The new resource also introduces a new look and an improved interface for searching for recipes.

Several guides describe the new resource and help you get started. Please take a look at:

In response to user requests we have added the following three new format converters to the GenomeSpace ecosystem.

CDT to GCT converts the CDT (cluster data table) output file from GenePattern's HierarchicalClustering module to GenePattern's more widely used GCT format. The converter preserves identifiers and expression values and removes any column or row that maps clustering tree relationships.

CDT to TAB converts the CDT output file from GenePattern's HierarchicalClustering module to Genomica TAB format. As with the GCT conversion above, the converter preserves identifiers and expression values and removes any column or row that maps clustering tree relationships.

LST to geneset.TAB converts a Genomica LST file to the Genomica geneset.TAB format. The description column of the LST file is removed and the output file defines the LST file's column of gene symbols as a single gene set in a tab-delimited format. Define additional gene sets by manually revising the geneset.TAB file.

We are pleased to announce that Cytoscape 3 in GenomeSpace has been updated to version 3.2.1. If you are already using an older version of Cytoscape 3, including the prior v3.1.1, manually upgrade to v3.2.1 using the installer at http://www.cytoscape.org/download.php. Upgrade is highly recommended. Once installed, the Cytoscape 3 tool icon will launch v3.2.1 from GenomeSpace. See full details in the Cytoscape v3.2.1 Release Notes.

Performance improvementsin v3.2

Quicker startup.

Faster network loading, merging, and rendering.

For developers, improved API for Tunables and Commands.

New features in v3.2

A built-in chart editor that now supports gradients. The chart editor renders node table data into high quality vector graphics that include the standard bar, box, line, pie, heatmap, and ring charts.

Interactive web visualization publishable as web applications.

System requirementsfor v3.2.1

All systems including Mac OS X 10.7 and Linux: install the latest version of Oracle Java. Cytoscape recommends Java 8 for v3.2 and v3.2.1 on all platforms, although Java 7 is still supported. Java 6 is no longer supported.

Windows XP and newer: 64 bit is recommended although 32 bit is still supported. Override default Oracle Java 32 bit installation for the 64 bit version by following instructions given in the v3.2.1 Release Notes.

Posted by Ted Liefeld, Kenneth Smith on Friday, January 30, 2015 at 09:50AM

We are pleased to announce that geWorkbench has been updated to version 2.6. In this updated version geWorkbench integration with GenomeSpace has been improved. Also it can now support larger datasets, has improved its use of BLAST and R, and has added the Classification and Regression Tree (CART) analysis from GenePattern. Full details are available in the geWorkbench release notes.

Note that since geWorkbench is a desktop application, launching it from GenomeSpace takes a few steps. Clicking launch in GenomeSpace will typically download a file to your computer (launchHelper.jnlp) which you need to save and then open manually to launch the application. This is common to all desktop applications due to browser security restrictions. Full details of the requirements for launching geWorkbench can be found on the geWorkbench wiki. There is also a useful post for adding Java runtime special exceptions to make launching geWorkbench easier.